Agricultural impacts on plant beneficial pseudomonads

Ruscoe, Heather and Dodd, Ian (2020) Agricultural impacts on plant beneficial pseudomonads. PhD thesis, Lancaster University.

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Abstract

The soil microbiome is a dynamic and complex environment that offers numerous ecosystem services. Beneficial Pseudomonas spp. are agriculturally relevant bacteria with a plethora of plant growth promoting (PGP) traits, making them desirable targets for microbial inoculant development. Microbial inoculants have typically failed to produce reliable results, which can be attributed to the introduction of microbes into ecologically unsuitable environments. Its therefore important to better understand factors that can alter Pseudomonas spp. community structure and functioning. Crop domestication and land management have both played important roles in the development of agriculture over the last 10,000 years, however they have been associated with negative impacts on the soil microbiome. Here, the impacts of these agricultural components on soil pseudomonads was investigated. The study of 17 domesticated and ancestral wheat genotypes cultivated in a grassland soil revealed no clear difference in pseudomonad community structure within rhizosphere or bulk soil. The Highfield experiment at Rothamsted Research tests the impact of land management and revealed various impacts to soil properties, wheat physiology and total microbial abundance across grassland, arable and bare fallow managed soils. However, pseudomonad abundance was not found to significantly differ in bulk soil and rhizosphere communities. Additional studies looking at the more closely associated root compartment of wheat grown in soils from distinct land uses, revealed differences in abundance and phylogeny of cultivated pseudomonads. A range of PGP genetic and functional potentials including siderophore production, anti-fungal activity and phosphate solubilisation differed in isolates according to land use. The presence of the 1-Aminocyclopropane-1-carboxylate (ACC) deaminase gene (acdS) was of particular interest, due to its potential to reduce levels of stress ethylene in plants by degrading its precursor ACC. Intriguingly, acdS gene abundance, phylogeny and functional activity appeared to differ in pseudomonads associated with the different land uses. The rhizosphere and root compartments of wheat had a higher acdS gene abundance, particularly in the bare fallow soil which is known to have degraded soil properties. This suggests factors associated with wheat grown in different land managements were driving the selection of ACC deaminase producing pseudomonads. In vitro attempts to promote wheat growth under salt stress by applying ACC deaminase-containing isolates was not successful. Overall this thesis evidences the functional potential of pseudomonads for use in microbial inoculants, whilst providing an insight into the complexity of soil-plant-microbe interactions.